Genomes and Genes
deuterium exchange measurement
Summary: A research technique to measure solvent exposed regions of molecules that is used to provide insight about PROTEIN CONFORMATION.
- Huang R, Garai K, Frieden C, Gross M. Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization. Biochemistry. 2011;50:9273-82 pubmed publisher..In addition, our results verify that ApoE4 is composed of a compact structure at its N-terminal domain. Regions of C-terminal domain, however, appear to lack defined structure. ..
- Cydzik M, Rudowska M, Stefanowicz P, Szewczuk Z. The competition of charge remote and charge directed fragmentation mechanisms in quaternary ammonium salt derivatized peptides--an isotopic exchange study. J Am Soc Mass Spectrom. 2011;22:2103-7 pubmed publisher..The isotopic labeling allows differentiation of fragments formed according to ChR and ChD mechanisms. ..
- Landgraf R, Chalmers M, Griffin P. Automated hydrogen/deuterium exchange electron transfer dissociation high resolution mass spectrometry measured at single-amide resolution. J Am Soc Mass Spectrom. 2012;23:301-9 pubmed publisher..We have applied this system to determine differential single amide resolution HDX data for the peroxizome proliferator activated receptor bound with two ligands of interest. ..
- Chalmers M, Busby S, Pascal B, West G, Griffin P. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev Proteomics. 2011;8:43-59 pubmed publisher..In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery. ..
- Percy A, Rey M, Burns K, Schriemer D. Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry-a review. Anal Chim Acta. 2012;721:7-21 pubmed publisher..Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided. ..
- Pascal B, Willis S, Lauer J, Landgraf R, West G, Marciano D, et al. HDX workbench: software for the analysis of H/D exchange MS data. J Am Soc Mass Spectrom. 2012;23:1512-21 pubmed publisher..The application is available at the project home page http://hdx.florida.scripps.edu . ..
- Hamuro Y, Coales S, Morrow J, Molnar K, Tuske S, Southern M, et al. Hydrogen/deuterium-exchange (H/D-Ex) of PPARgamma LBD in the presence of various modulators. Protein Sci. 2006;15:1883-92 pubmed..The results showed that the change in protein dynamics induced by ligand binding may be an important factor for the activation of genes and that H/D-Ex is a useful method for analyzing the biological activity of drug leads. ..
- Hodkinson J, Jahn T, Radford S, Ashcroft A. HDX-ESI-MS reveals enhanced conformational dynamics of the amyloidogenic protein beta(2)-microglobulin upon release from the MHC-1. J Am Soc Mass Spectrom. 2009;20:278-86 pubmed publisher..Thus, upon dissociation from the stabilizing influence of the MHC-1, free beta(2)m becomes highly dynamic and undergoes unfolding transitions that result in an aggregation-competent protein. ..
- Spraggon G, Pantazatos D, Klock H, Wilson I, Woods V, Lesley S. On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171. Protein Sci. 2004;13:3187-99 pubmed publisher..The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed...
- Ferraro D, Lazo N, Robertson A. EX1 hydrogen exchange and protein folding. Biochemistry. 2004;43:587-94 pubmed..However, key questions remain regarding the interpretation of EX1 hydrogen exchange. ..
- Dai S, Burris T, Dodge J, Montrose Rafizadeh C, Wang Y, Pascal B, et al. Unique ligand binding patterns between estrogen receptor alpha and beta revealed by hydrogen-deuterium exchange. Biochemistry. 2009;48:9668-76 pubmed publisher..The compound-specific perturbations in HDX kinetics observed for each of the two isoforms should aid the development of subtype-selective ER ligands. ..
- Engen J. Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS. Anal Chem. 2009;81:7870-5 pubmed publisher..Recent technological advances have led to improvements in the technique, but has this goal yet been achieved? (To listen to a podcast about this Feature, please go to the Analytical Chemistry Web site at pubs.acs.org/journal/ancham.). ..
- Bennett B, Langan P, Coates L, Mustyakimov M, Schoenborn B, Howell E, et al. Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc Natl Acad Sci U S A. 2006;103:18493-8 pubmed..Several D(2)Os are observed at hydrophobic surfaces, including two pockets near the MTX-binding site. A previously unidentified D(2)O hydrogen bonds with the catalytic D27 in mon. B, stabilizing its negative charge. ..
- Ortiz M, Sanoguet Z, Hu H, Chazin W, McMurray C, McMurray C, et al. Dynamics of hydrogen-deuterium exchange in Chlamydomonas centrin. Biochemistry. 2005;44:2409-18 pubmed
- Brock M, Fan F, Mei F, Li S, Gessner C, Woods V, et al. Conformational analysis of Epac activation using amide hydrogen/deuterium exchange mass spectrometry. J Biol Chem. 2007;282:32256-63 pubmed
- Heegaard N, Jørgensen T, Rozlosnik N, Corlin D, Pedersen J, Tempesta A, et al. Unfolding, aggregation, and seeded amyloid formation of lysine-58-cleaved beta 2-microglobulin. Biochemistry. 2005;44:4397-407 pubmed
- Burke J, Babakhani A, Gorfe A, Kokotos G, Li S, Woods V, et al. Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry. J Am Chem Soc. 2009;131:8083-91 pubmed publisher..This combination of computational and experimental methods is useful in defining more accurate inhibitor binding sites and can be used in the generation of better inhibitors against GIVA PLA(2). ..
- Sharma S, Zheng H, Huang Y, Ertekin A, Hamuro Y, Rossi P, et al. Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry. Proteins. 2009;76:882-94 pubmed publisher..Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. ..
- Liang Z, Tsigos I, Lee T, Bouriotis V, Resing K, Ahn N, et al. Evidence for increased local flexibility in psychrophilic alcohol dehydrogenase relative to its thermophilic homologue. Biochemistry. 2004;43:14676-83 pubmed..The structural factors underlying the differences in local protein flexibility and catalysis between htADH and psADH are discussed in conjunction with results from crystallographic and fluorescence spectroscopy studies. ..
- Frantom P, Zhang H, Emmett M, Marshall A, Blanchard J. Mapping of the allosteric network in the regulation of alpha-isopropylmalate synthase from Mycobacterium tuberculosis by the feedback inhibitor L-leucine: solution-phase H/D exchange monitored by FT-ICR mass spectrometry. Biochemistry. 2009;48:7457-64 pubmed publisher
- Hamuro Y, Anand G, Kim J, Juliano C, Stranz D, Taylor S, et al. Mapping intersubunit interactions of the regulatory subunit (RIalpha) in the type I holoenzyme of protein kinase A by amide hydrogen/deuterium exchange mass spectrometry (DXMS). J Mol Biol. 2004;340:1185-96 pubmed..Furthermore, the difference in the protection patterns between RIalpha and the previously studied RIIbeta upon cAMP-binding suggests isoform-specific differences in cAMP-dependent regulation of PKA activity. ..
- Hossain B, Konermann L. Pulsed hydrogen/deuterium exchange MS/MS for studying the relationship between noncovalent protein complexes in solution and in the gas phase after electrospray ionization. Anal Chem. 2006;78:1613-9 pubmed..Overall, it appears that the pulsed HDX MS/MS approach introduced in this work represents a widely applicable tool for deciphering the relationship between ESI mass spectra and protein quaternary structures in solution. ..
- Hotchko M, Anand G, Komives E, Ten Eyck L. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 2006;15:583-601 pubmed..Finally, a method for determining the back exchange corrected populations is presented, and its effect on the data is discussed under various circumstances. ..
- Yamamoto T, Izumi S, Gekko K. Mass spectrometry on segment-specific hydrogen exchange of dihydrofolate reductase. J Biochem. 2004;135:17-24 pubmed
- Black B, Foltz D, Chakravarthy S, Luger K, Woods V, Cleveland D. Structural determinants for generating centromeric chromatin. Nature. 2004;430:578-82 pubmed..Thus, the centromere-targeting domain of CENP-A confers a unique structural rigidity to the nucleosomes into which it assembles, and is likely to have a role in maintaining centromere identity. ..
- Tong Y, Wuebbens M, Rajagopalan K, Fitzgerald M. Thermodynamic analysis of subunit interactions in Escherichia coli molybdopterin synthase. Biochemistry. 2005;44:2595-601 pubmed
- Kheterpal I, Cook K, Wetzel R. Hydrogen/deuterium exchange mass spectrometry analysis of protein aggregates. Methods Enzymol. 2006;413:140-66 pubmed..These data provide insights into the structures of monomers, protofibrils, and fibrils and to the structural relations among these states. ..
- Pascal B, Chalmers M, Busby S, Mader C, Southern M, Tsinoremas N, et al. The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data. BMC Bioinformatics. 2007;8:156 pubmed..Integration of the different components of The Deuterator coupled with the flexibility of common data file formats allow this system to be accessible to the broadening H/D exchange community. ..
- Hamuro Y, Coales S, Southern M, Nemeth Cawley J, Stranz D, Griffin P. Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J Biomol Tech. 2003;14:171-82 pubmed
- Zhang H, Bou Assaf G, Emmett M, Marshall A. Fast reversed-phase liquid chromatography to reduce back exchange and increase throughput in H/D exchange monitored by FT-ICR mass spectrometry. J Am Soc Mass Spectrom. 2009;20:520-4 pubmed publisher..The rapid separation coupled with high-resolution FT-ICR MS at 14.5 T provides high amino acid sequence coverage, high sample throughput, and high reproducibility and reliability. ..
- Rennella E, Corazza A, Fogolari F, Viglino P, Giorgetti S, Stoppini M, et al. Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange. Biophys J. 2009;96:169-79 pubmed publisher..e., global unfolding in the core region and partial openings of the native state, determine the observed exchange rates. These findings are analyzed with respect to the amyloidogenic properties of the protein. ..
- Bennett B, Gardberg A, Blair M, Dealwis C. On the determinants of amide backbone exchange in proteins: a neutron crystallographic comparative study. Acta Crystallogr D Biol Crystallogr. 2008;D64:764-83 pubmed publisher..For some structures, the constituents of the hydrophobic protein core could be identified based on contiguous regions that are resistant to exchange and have significant depth. These may, in fact, constitute minimal folding domains. ..
- Nikamanon P, Pun E, Chou W, Koter M, Gershon P. "TOF2H": a precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinformatics. 2008;9:387 pubmed publisher..It runs in a standard MS Windows (XP or Vista) environment, and can be downloaded http://tof2h.bio.uci.edu or obtained from the authors at no cost. ..
- Slysz G, Baker C, Bozsa B, Dang A, Percy A, Bennett M, et al. Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. BMC Bioinformatics. 2009;10:162 pubmed publisher..The ability to accommodate the tandem MS dimension supports alternative data collection and analysis strategies, as well as higher resolution localization of deuteration where permitted by the fragmentation mechanism. ..
- Slysz G, Percy A, Schriemer D. Restraining expansion of the peak envelope in H/D exchange-MS and its application in detecting perturbations of protein structure/dynamics. Anal Chem. 2008;80:7004-11 pubmed publisher..0 +/- 1.1 (apo-CaM) and 1.4 +/- 1.3% (holo-CaM) using 10% D 2O in the labeling experiment. Further, only two peaks of a peptide peak distribution are needed to sensitively monitor changes in protein structure, dynamics, or both. ..
- Xu M, Shashilov V, Lednev I. Probing the cross-beta core structure of amyloid fibrils by hydrogen-deuterium exchange deep ultraviolet resonance Raman spectroscopy. J Am Chem Soc. 2007;129:11002-3 pubmed
- Nazabal A, Schmitter J. Hydrogen-deuterium exchange analyzed by matrix-assisted laser desorption-ionization mass spectrometry and the HET-s prion model. Methods Enzymol. 2006;413:167-81 pubmed..The combined advantages of these two instruments yield a suitable solution for HXMS experiments that require highly resolved peptide mass fingerprints, high sensitivity, and speed of analysis for deuterium incorporation measurements. ..
- Englander S. Hydrogen exchange and mass spectrometry: A historical perspective. J Am Soc Mass Spectrom. 2006;17:1481-1489 pubmed publisher..This article briefly reviews the advances that have led us to this point and the understanding that has so far been achieved. ..
- Yang J, Garrod S, Deal M, Anand G, Woods V, Taylor S. Allosteric network of cAMP-dependent protein kinase revealed by mutation of Tyr204 in the P+1 loop. J Mol Biol. 2005;346:191-201 pubmed..All these observations lead to an interesting new way to view the structural architecture and allosteric conformational regulation of the protein kinase molecule. ..
- Villanueva J, Hoshino M, Katou H, Kardos J, Hasegawa K, Naiki H, et al. Increase in the conformational flexibility of beta 2-microglobulin upon copper binding: a possible role for copper in dialysis-related amyloidosis. Protein Sci. 2004;13:797-809 pubmed..This may contribute to the overall destabilization of the molecule, increasing the equilibrium population of the amyloidogenic intermediate. ..
- Zhang H, Kazazic S, Schaub T, Tipton J, Emmett M, Marshall A. Enhanced digestion efficiency, peptide ionization efficiency, and sequence resolution for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem. 2008;80:9034-41 pubmed..Such assignments of highly overlapped fragments promise to greatly enhance the accuracy and sequence resolution for determining conformational differences resulting from ligand binding or protein-protein interactions. ..
- Pascal B, Chalmers M, Busby S, Griffin P. HD desktop: an integrated platform for the analysis and visualization of H/D exchange data. J Am Soc Mass Spectrom. 2009;20:601-10 pubmed publisher..florida.scripps.edu. ..
- Liu Y, Konermann L. Enzyme conformational dynamics during catalysis and in the 'resting state' monitored by hydrogen/deuterium exchange mass spectrometry. FEBS Lett. 2006;580:5137-42 pubmed..This finding implies that the conformational dynamics that mediate HDX are not significantly different in the resting state of the enzyme and during substrate turnover. ..
- Olofsson A, Sauer Eriksson A, Ohman A. The solvent protection of alzheimer amyloid-beta-(1-42) fibrils as determined by solution NMR spectroscopy. J Biol Chem. 2006;281:477-83 pubmed..Consequently, our findings provide a molecular explanation for the increased amyloidogenicity and toxicity of Abeta-(1-42) compared with shorter Abeta variants found in vivo. ..
- Eyles S, Kaltashov I. Methods to study protein dynamics and folding by mass spectrometry. Methods. 2004;34:88-99 pubmed..In this paper, we describe several applications of these methodologies to probe the dynamic events key to the structure, folding, and biological functions of proteins. ..
- Cravello L, Lascoux D, Forest E. Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins. Rapid Commun Mass Spectrom. 2003;17:2387-93 pubmed..Furthermore, we obtained a better spatial resolution for deuterium incorporation data, specifying accurately the deuterated regions. ..